||5-hydroxymethyluracil (HOMeU) is found as natural base in genomic DNA of dinoflagellates in addition to the four standard bases, but not in any other groups of eukaryotes. It replaces a fraction of thymine and distributes non-randomly in DNA. However, little is known about its biosynthesis and biological function. Here I present that HOMeU is most likely synthesized through the modification of thymine on polynucleotide level in dinoflagellates. In searching the enzymes that catalyze its biosynthesis, a protein belonging to Fe (Ⅱ)-, α-ketoglutarate- dependent dioxygenase superfamily was identified, which is shown to have the property to be expected of catalyzing the conversion of thymine to HOMeU on DNA strand in the presence of some unknown cofactors. I also want to investigate whether HOMeU in DNA is conducive to the formation of liquid crystalline DNA in dinoflagellates, the relationship between HOMeU content in DNA and the intensity of birefringence (a parameter of liquid crystal DNA) was examined, but no significant correlation was found. On the other hand, DNA condensation experiment in vitro showed the presence of HOMeU in DNA was conducive to the transition of isotropic to anisotropic phase and promoted DNA condensation. At the end, I discuss why the presence of HOMeU in dinoflagellates is so unique in eukaryotic world.